comparison preprocessing.xml @ 3:4ecdea4cbea1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984

2:48d9421bf176

    min_frag_size = $method.min_frag_size,
    #end if
    #if $method.max_frag_size
    max_frag_size = $method.max_frag_size,
    #end if
    ##counting_strategy = '$method.counting_strategy',
    count_frag_as_reads = $method.count_frag_as_reads,
    n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
)

#else if $method.method == 'pp.make_gene_matrix'
adata = sa.pp.make_gene_matrix(

    min_frag_size = $method.min_frag_size,
    #end if
    #if $method.max_frag_size
    max_frag_size = $method.max_frag_size,
    #end if
    ##counting_strategy = '$method.counting_strategy'
    count_frag_as_reads = $method.count_frag_as_reads
)

#else if $method.method == 'pp.filter_cells'
sa.pp.filter_cells(
    adata,

                <expand macro="param_chunk_size" size="500"/>
                <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="min_max_frag_size"/>
                <!--expand macro="param_counting_strategy"/-->
                <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
            </when>
            <when value="pp.make_gene_matrix">
                <expand macro="inputs_anndata"/>
                <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
                <expand macro="param_chunk_size" size="500"/>

                <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
                <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
                <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
                <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
                <expand macro="min_max_frag_size"/>
                <!--expand macro="param_counting_strategy"/-->
                <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
            </when>
            <when value="pp.filter_cells">
                <expand macro="inputs_anndata"/>
                <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
                <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>

                <param name="id_type" value="gene"/>
                <param name="transcript_name_key" value="transcript_name"/>
                <param name="transcript_id_key" value="transcript_id"/>
                <param name="gene_name_key" value="gene_name"/>
                <param name="gene_id_key" value="gene_id"/>
                <param name="count_frag_as_reads" value="True"/>
                </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">

                    <has_text_matching expression="id_type = 'gene'"/>
                    <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
                    <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
                    <has_text_matching expression="gene_name_key = 'gene_name'"/>
                    <has_text_matching expression="gene_id_key = 'gene_id'"/>
                    <has_text_matching expression="count_frag_as_reads = True"/>
                </assert_contents>
            </output>
            <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
        </test>
        <test expect_num_outputs="2">

                <param name="method" value="pp.add_tile_matrix"/>
                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
                <param name="bin_size" value="5000"/>
                <param name="chunk_size" value="500"/>
                <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
                <param name="count_frag_as_reads" value="True"/>
                </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sa.pp.add_tile_matrix"/>
                    <has_text_matching expression="bin_size = 5000"/>
                    <has_text_matching expression="chunk_size = 500"/>
                    <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
                    <has_text_matching expression="count_frag_as_reads = True"/>
                </assert_contents>
            </output>
            <output name="anndata_out"  ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
        </test>
        <test expect_num_outputs="2">

3:4ecdea4cbea1

    min_frag_size = $method.min_frag_size,
    #end if
    #if $method.max_frag_size
    max_frag_size = $method.max_frag_size,
    #end if
    counting_strategy = '$method.counting_strategy',
    n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
)

#else if $method.method == 'pp.make_gene_matrix'
adata = sa.pp.make_gene_matrix(

    min_frag_size = $method.min_frag_size,
    #end if
    #if $method.max_frag_size
    max_frag_size = $method.max_frag_size,
    #end if
    counting_strategy = '$method.counting_strategy'
)

#else if $method.method == 'pp.filter_cells'
sa.pp.filter_cells(
    adata,

                <expand macro="param_chunk_size" size="500"/>
                <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
                    <expand macro="sanitize_query"/>
                </param>
                <expand macro="min_max_frag_size"/>
                <expand macro="param_counting_strategy"/>
            </when>
            <when value="pp.make_gene_matrix">
                <expand macro="inputs_anndata"/>
                <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
                <expand macro="param_chunk_size" size="500"/>

                <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
                <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
                <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
                <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
                <expand macro="min_max_frag_size"/>
                <expand macro="param_counting_strategy"/>
            </when>
            <when value="pp.filter_cells">
                <expand macro="inputs_anndata"/>
                <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
                <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>

                <param name="id_type" value="gene"/>
                <param name="transcript_name_key" value="transcript_name"/>
                <param name="transcript_id_key" value="transcript_id"/>
                <param name="gene_name_key" value="gene_name"/>
                <param name="gene_id_key" value="gene_id"/>
                <param name="counting_strategy" value="insertion"/>
                </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">

                    <has_text_matching expression="id_type = 'gene'"/>
                    <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
                    <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
                    <has_text_matching expression="gene_name_key = 'gene_name'"/>
                    <has_text_matching expression="gene_id_key = 'gene_id'"/>
                    <has_text_matching expression="counting_strategy = 'insertion'"/>
                </assert_contents>
            </output>
            <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
        </test>
        <test expect_num_outputs="2">

                <param name="method" value="pp.add_tile_matrix"/>
                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
                <param name="bin_size" value="5000"/>
                <param name="chunk_size" value="500"/>
                <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
                <param name="counting_strategy" value="insertion"/>
                </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sa.pp.add_tile_matrix"/>
                    <has_text_matching expression="bin_size = 5000"/>
                    <has_text_matching expression="chunk_size = 500"/>
                    <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
                    <has_text_matching expression="counting_strategy = 'insertion'"/>
                </assert_contents>
            </output>
            <output name="anndata_out"  ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
        </test>
        <test expect_num_outputs="2">
            <!-- pp.add_tile_matrix counting_strategy fragment -->
            <conditional name="method">
                <param name="method" value="pp.add_tile_matrix"/>
                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
                <param name="bin_size" value="5000"/>
                <param name="chunk_size" value="500"/>
                <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
                <param name="counting_strategy" value="fragment"/>
                </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="hidden_output">
                <assert_contents>
                    <has_text_matching expression="sa.pp.add_tile_matrix"/>
                    <has_text_matching expression="bin_size = 5000"/>
                    <has_text_matching expression="chunk_size = 500"/>
                    <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
                    <has_text_matching expression="counting_strategy = 'fragment'"/>
                </assert_contents>
            </output>
            <output name="anndata_out"  ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
        </test>
        <test expect_num_outputs="2">